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Integrated Database of Microbial Genomes and Cellular Functions

Research Project

Project/Area Number 15013227
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyoto University

Principal Investigator

KANEHISA Minoru  Kyoto University, Institute for Chemical Research, Professor, 化学研究所, 教授 (70183275)

Co-Investigator(Kenkyū-buntansha) KAWASHIMA Shuichi  University of Tokyo, Institute of Medical Science, Instructor, 医科学研究所, 助手 (50314274)
KATAYAMA Toshiaki  University of Tokyo, Institute of Medical Science, Instructor, 医科学研究所, 助手 (60396869)
Project Period (FY) 2003 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥24,000,000 (Direct Cost: ¥24,000,000)
Fiscal Year 2004: ¥12,000,000 (Direct Cost: ¥12,000,000)
Fiscal Year 2003: ¥12,000,000 (Direct Cost: ¥12,000,000)
KeywordsGenome database / Bioinformatics / Systems biology / Microarray analysis / Comparative genome analysis / Pathway analysis / マイクロアレイ / オーソログ解析 / 機能予測
Research Abstract

The roles of biological databases are changing in two important aspects to meet the needs for understanding biological systems from genomic information. First, the data contents about molecular sequences, molecular structures, and molecular functions are certainly not sufficient. It is necessary to somehow capture higher-level structures and functions, such as molecular interaction networks and cellular processes, and create new databases that integrate both molecular and higher-level information. Second, although the current mechanism of data submissions by individual authors works well for the sequence and 3D structure databases, it is not appropriate for keeping up with the expanding biological knowledge in the research community. In this project we developed BSORF (bacillus.genome.jp) and CYORF (cyano.genome.jp) databases for the Bacillus subtilis and cyanobacteria research communities, respectively. For the first aspect we utilized our KEGG resource for pathway and network information, which is highly integrated with the BSORF and CYORF databases. In addition, BSORF contains a large set of microarray gene expression data and information about essential genes, both of which were obtained by the Japanese research community. For the second aspect, we have been promoting the mechanism of community annotation database where individual researchers in the community not only obtain information from the database, but also enter their knowledge into the database, so that the community as a whole can share most up-to-date information and knowledge. CYORF is the most successful community annotation database, which is now widely accepted by the international cyanobacteria research community. We also developed comparative genomics tools for automatic classification of orthologous genes and for detection of conserved gene clusters in multiple genomes. Both tools are made available in KEGG (www.genome.jp/kegg/).

Report

(3 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • Research Products

    (16 results)

All 2005 2004 Other

All Journal Article (11 results) Publications (5 results)

  • [Journal Article] Fast and accurate database homology search using upper bounds of local alignment scores.2005

    • Author(s)
      Itoh, M., Goto, S., Akutsu, T., Kanehisa, M.
    • Journal Title

      Bioinformatics 21

      Pages: 912-921

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Supervised enzyme network inference from the integration of genomic data and chemical information.2005

    • Author(s)
      Yamanishi, Y., Vert, J.-P., Kanehisa, M.
    • Journal Title

      Bioinformatics 21

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Fast and accurate database homology search using upper bounds of local alignment scores.2005

    • Author(s)
      Itoh, M., Goto, S., Akutsu, T., Kanehisa, M
    • Journal Title

      Bioinformatics 20(in press)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Clustering of database sequences for fast homology search using upper bounds on alignment score.2004

    • Author(s)
      Itoh, M., Akutsu, T., Kanehisa, M.
    • Journal Title

      Genome Informatics 15

      Pages: 93-104

    • NAID

      130003812084

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Annual Research Report 2004 Final Research Report Summary
  • [Journal Article] Protein network inference from multiple genomic data : a supervised approach.2004

    • Author(s)
      Yamanishi, Y., Vert, J.-P., Kanehisa, M.
    • Journal Title

      Bioinformatics 20

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes.2004

    • Author(s)
      Igarashi, Y., Aoki, K.F., Mamitsuka, H., Kuma, K., Kanehisa, M.
    • Journal Title

      Mol. Biol. Evol. 21

      Pages: 2149-2160

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Clustering of database sequences for fast homology search using upper bounds on alignment score.2004

    • Author(s)
      Itoh, M., Akutsu, T., Kanehisa, M.
    • Journal Title

      Genome Informatics 15(1)

      Pages: 93-104

    • NAID

      130003812084

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes.2004

    • Author(s)
      Igarashi, Y., Aoki, K.F., Mamitsuka, H., Kuma, K., Kanehisa, M.
    • Journal Title

      Mol.Biol.Evol. 21

      Pages: 2149-2160

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Using protein motif combinations to update KEGG pathway maps and orthologue tables.2004

    • Author(s)
      Nikitin, F., Rance, B., Itoh, M., Kanehisa, M., Lisacek, F.
    • Journal Title

      Genome Informatics 15

      Pages: 266-275

    • NAID

      130003997370

    • Related Report
      2004 Annual Research Report
  • [Journal Article] The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domain's in eukaryotes and prokaryotes.2004

    • Author(s)
      Igarashi, Y., Aoki, K.F., Mamitsuka, H., Kuma, K., Kanehisa.M.
    • Journal Title

      Mol.Biol.Evol. 21

      Pages: 2149-2160

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Extraction of phylogenetic network modules from prokayrote metabolic pathways.2004

    • Author(s)
      Yamada, T., Goto, S., Kanehisa, M.
    • Journal Title

      Genome Informatics 15

      Pages: 249-258

    • NAID

      130003812098

    • Related Report
      2004 Annual Research Report
  • [Publications] Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: "The KEGG resource for deciphering the genome"Nucleic Acids Res. 32. D277-D280 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] Vert, J.-P., Kanehisa, M.: "Extracting active pathways from gene expression data"Bioinformatics. 19. ii238-ii234 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Park, K.-J., Kanehisa, M.: "Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs"Bioinformatics. 19. 1656-1663 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yamanishi, Y., Vert, J.-P., Kanehisa, M.: "Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis"Bioinformatics. 19. i323-i330 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Kanehisa, M., Bork, P.: "Bioinformatics in the post-sequence era"Nature Genetics. 33. 305-310 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2018-03-28  

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